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Liang Y, Zhou Y, Xie D, Yin F, Luo X. Hypermethylation and low expression of FANCC involved in multi-walled carbon nanotube-induced toxicity on ARPE-19 cells. ENVIRONMENTAL RESEARCH 2024; 241:117619. [PMID: 37952855 DOI: 10.1016/j.envres.2023.117619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Multi-walled carbon nanotube (MWCNT) exposure was observed to cause damages on the viability of ocular cells, however, the underlying mechanisms remain not well understood. Epigenetic alterations that regulate gene expression have been identified as a major responsiveness to environmental challenge. Thus, the aim of this study was to screen methylation-regulated genes involved in MWCNT exposure. The Illumina Human Methylation 850 K array was employed to determine the genome-wide DNA methylation profile of human retinal pigment epithelial cell line (ARPE-19) exposed to 50% inhibition concentration of MWCNTs (100 μg/ml) for 24 h or without (n = 3 for each group). Then, the transcriptome data obtained by high-throughput RNA sequencing previously were integrated with DNA methylome to identify the overlapped genes. As a result, the integrative bioinformatics analysis identified that compared with controls, FA complementation group C (FANCC) was hypermethylated and downregulated in MWCNT-exposed ARPE-19 cells. Quantitative real-time polymerase chain reaction analysis confirmed the mRNA expression level of FANCC was significantly decreased following MWCNT treatment and the addition of DNA methylation inhibitor 5-Aza-deoxycytidine (10 μM) reversed this decrease. Pyrosequencing analysis further validated the hypermethylation status at the 5'-untranslated promoter region of FANCC (cg14583550) in MWCNT-exposed ARPE-19 cells. Protein-protein interaction network and function analyses predicted that FANCC may contribute to MWCNT-induced cytotoxicity by interacting with heat shock protein 90 beta family member 1 and then upregulating cytokine interleukin-6 and apoptosis biomarker caspase 3. In conclusion, the present study links the epigenetic modification of FANCC with the pathogenesis of MWCNT-induced retinal toxicity.
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Affiliation(s)
- Yunxia Liang
- College of Textile and Clothing Engineering, Soochow University, 199 Ren-Ai Road, Suzhou, 215123, China
| | - Yang Zhou
- School of Textile Science and Engineering/State Key Laboratory of New Textile Materials and Advanced Processing Technology, Wuhan Textile University, Wuhan, 430200, China.
| | - Dongli Xie
- College of Textile and Clothing Engineering, Soochow University, 199 Ren-Ai Road, Suzhou, 215123, China
| | - Fei Yin
- College of Textile and Clothing Engineering, Soochow University, 199 Ren-Ai Road, Suzhou, 215123, China
| | - Xiaogang Luo
- College of Textile and Clothing Engineering, Soochow University, 199 Ren-Ai Road, Suzhou, 215123, China.
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Hautanen V, Morikka J, Saarimäki LA, Bisenberger J, Toimela T, Serra A, Greco D. The in vitro immunomodulatory effect of multi-walled carbon nanotubes by multilayer analysis. NANOIMPACT 2023; 31:100476. [PMID: 37437691 DOI: 10.1016/j.impact.2023.100476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/17/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
The study of multi-walled carbon nanotube (MWCNT) induced immunotoxicity is crucial for determining hazards posed to human health. MWCNT exposure most commonly occurs via the airways, where macrophages are first line responders. Here we exploit an in vitro assay, measuring dose-dependent secretion of a wide panel of cytokines, as a measure of immunotoxicity following the non-lethal, multi-dose exposure (IC5, IC10 and IC20) to 7 MWCNTs with different intrinsic properties. We find that a tangled structure, and small aspect ratio are key properties predicting MWCNT induced immunotoxicity, mediated predominantly by IL1B cytokine secretion. To assess the mechanism of action giving rise to MWCNT immunotoxicity, transcriptomics analysis was linked to cytokine secretion in a multilayer model established through correlation analysis across exposure concentrations. This reinforced the finding that tangled MWCNTs have greater immunomodulatory potency, displaying enrichment of immune system, signal transduction and pattern recognition associated pathways. Together our results further elucidate how structure, length and aspect ratio, critical intrinsic properties of MWCNTs, are tied to immunotoxicity.
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Affiliation(s)
- Veera Hautanen
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere 33520, Finland; Institute of Biotechnology, University of Helsinki, P.O.Box 56, Helsinki, Uusimaa 00014, Finland
| | - Jack Morikka
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere 33520, Finland
| | - Laura Aliisa Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere 33520, Finland
| | - Jan Bisenberger
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere 33520, Finland
| | - Tarja Toimela
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere 33520, Finland
| | - Angela Serra
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere 33520, Finland; Tampere Institute for Advanced Study, Tampere University, Kalevantie 4, Tampere 33100, Finland
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere 33520, Finland; Institute of Biotechnology, University of Helsinki, P.O.Box 56, Helsinki, Uusimaa 00014, Finland; Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Finland.
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Erdem JS, Závodná T, Ervik TK, Skare Ø, Hron T, Anmarkrud KH, Kuśnierczyk A, Catalán J, Ellingsen DG, Topinka J, Zienolddiny-Narui S. High aspect ratio nanomaterial-induced macrophage polarization is mediated by changes in miRNA levels. Front Immunol 2023; 14:1111123. [PMID: 36776851 PMCID: PMC9911541 DOI: 10.3389/fimmu.2023.1111123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
Introduction Inhalation of nanomaterials may induce inflammation in the lung which if left unresolved can manifest in pulmonary fibrosis. In these processes, alveolar macrophages have an essential role and timely modulation of the macrophage phenotype is imperative in the onset and resolution of inflammatory responses. This study aimed to investigate, the immunomodulating properties of two industrially relevant high aspect ratio nanomaterials, namely nanocellulose and multiwalled carbon nanotubes (MWCNT), in an alveolar macrophage model. Methods MH-S alveolar macrophages were exposed at air-liquid interface to cellulose nanocrystals (CNC), cellulose nanofibers (CNF) and two MWCNT (NM-400 and NM-401). Following exposure, changes in macrophage polarization markers and secretion of inflammatory cytokines were analyzed. Furthermore, the potential contribution of epigenetic regulation in nanomaterial-induced macrophage polarization was investigated by assessing changes in epigenetic regulatory enzymes, miRNAs, and rRNA modifications. Results Our data illustrate that the investigated nanomaterials trigger phenotypic changes in alveolar macrophages, where CNF exposure leads to enhanced M1 phenotype and MWCNT promotes M2 phenotype. Furthermore, MWCNT exposure induced more prominent epigenetic regulatory events with changes in the expression of histone modification and DNA methylation enzymes as well as in miRNA transcript levels. MWCNT-enhanced changes in the macrophage phenotype were correlated with prominent downregulation of the histone methyltransferases Kmt2a and Smyd5 and histone deacetylases Hdac4, Hdac9 and Sirt1 indicating that both histone methylation and acetylation events may be critical in the Th2 responses to MWCNT. Furthermore, MWCNT as well as CNF exposure led to altered miRNA levels, where miR-155-5p, miR-16-1-3p, miR-25-3p, and miR-27a-5p were significantly regulated by both materials. PANTHER pathway analysis of the identified miRNA targets showed that both materials affected growth factor (PDGF, EGF and FGF), Ras/MAPKs, CCKR, GnRH-R, integrin, and endothelin signaling pathways. These pathways are important in inflammation or in the activation, polarization, migration, and regulation of phagocytic capacity of macrophages. In addition, pathways involved in interleukin, WNT and TGFB signaling were highly enriched following MWCNT exposure. Conclusion Together, these data support the importance of macrophage phenotypic changes in the onset and resolution of inflammation and identify epigenetic patterns in macrophages which may be critical in nanomaterial-induced inflammation and fibrosis.
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Affiliation(s)
- Johanna Samulin Erdem
- National Institute of Occupational Health, Oslo, Norway,*Correspondence: Johanna Samulin Erdem,
| | - Táňa Závodná
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine, the Czech Academy of Sciences, Prague, Czechia
| | | | - Øivind Skare
- National Institute of Occupational Health, Oslo, Norway
| | - Tomáš Hron
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czechia
| | | | - Anna Kuśnierczyk
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway,Proteomics and Modomics Experimental Core Facility and St. Olavs Hospital Central Staff, Trondheim, Norway
| | - Julia Catalán
- Department of Work Safety, Finnish Institute of Occupational Health, Helsinki, Finland,Department of Anatomy, Embryology and Genetics, University of Zaragoza, Zaragoza, Spain
| | | | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine, the Czech Academy of Sciences, Prague, Czechia
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da Costa Siqueira JT, Reis AC, Lopes JML, Ladeira LO, Viccini LF, de Mello Brandão H, Munk M, de Sousa SM. Chromosomal aberrations and changes in the methylation patterns of Lactuca sativa L. (Asteraceae) exposed to carbon nanotubes. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01325-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Serra A, Saarimäki LA, Pavel A, del Giudice G, Fratello M, Cattelani L, Federico A, Laurino O, Marwah VS, Fortino V, Scala G, Sofia Kinaret PA, Greco D. Nextcast: a software suite to analyse and model toxicogenomics data. Comput Struct Biotechnol J 2022; 20:1413-1426. [PMID: 35386103 PMCID: PMC8956870 DOI: 10.1016/j.csbj.2022.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 11/28/2022] Open
Abstract
Toxicogenomics is emerging as a valid approach to characterise the mechanism of action of chemicals. Structured pipelines for toxicogenomics increase standardisation and regulatory acceptance. We developed the Nextcast software suite for robust analysis and modelling of toxicogenomic data. Nextcast offers customisable modular pipelines to tackle multiple biological questions.
The recent advancements in toxicogenomics have led to the availability of large omics data sets, representing the starting point for studying the exposure mechanism of action and identifying candidate biomarkers for toxicity prediction. The current lack of standard methods in data generation and analysis hampers the full exploitation of toxicogenomics-based evidence in regulatory risk assessment. Moreover, the pipelines for the preprocessing and downstream analyses of toxicogenomic data sets can be quite challenging to implement. During the years, we have developed a number of software packages to address specific questions related to multiple steps of toxicogenomics data analysis and modelling. In this review we present the Nextcast software collection and discuss how its individual tools can be combined into efficient pipelines to answer specific biological questions. Nextcast components are of great support to the scientific community for analysing and interpreting large data sets for the toxicity evaluation of compounds in an unbiased, straightforward, and reliable manner. The Nextcast software suite is available at: ( https://github.com/fhaive/nextcast).
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Affiliation(s)
- Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Laura Aliisa Saarimäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Alisa Pavel
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Giusy del Giudice
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Michele Fratello
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Luca Cattelani
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | | | - Veer Singh Marwah
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Giovanni Scala
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Pia Anneli Sofia Kinaret
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere University, Tampere, Finland
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Corresponding author.
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